Starting phenix.real_space_refine on Sun Mar 17 23:39:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/03_2024/6rbg_4798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/03_2024/6rbg_4798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/03_2024/6rbg_4798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/03_2024/6rbg_4798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/03_2024/6rbg_4798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/03_2024/6rbg_4798.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 12216 2.51 5 N 3344 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 271": "OD1" <-> "OD2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E ASP 291": "OD1" <-> "OD2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F ASP 291": "OD1" <-> "OD2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ASP 223": "OD1" <-> "OD2" Residue "G PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 271": "OD1" <-> "OD2" Residue "G ASP 291": "OD1" <-> "OD2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 271": "OD1" <-> "OD2" Residue "H ASP 291": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "B" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "C" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "D" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "E" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "F" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "G" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "H" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Time building chain proxies: 10.32, per 1000 atoms: 0.53 Number of scatterers: 19336 At special positions: 0 Unit cell: (111.3, 111.3, 166.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3720 8.00 N 3344 7.00 C 12216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 3.6 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 60.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA A 85 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.586A pdb=" N LYS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 183 through 210 removed outlier: 3.631A pdb=" N VAL A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 230 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 232' Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 155 " --> pdb=" O TYR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.706A pdb=" N LEU B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 230 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 232' Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 320 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA C 85 " --> pdb=" O GLY C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.588A pdb=" N LYS C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 183 through 210 removed outlier: 3.633A pdb=" N VAL C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE C 230 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 232' Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 80 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.632A pdb=" N GLN D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU D 229 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 230 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 231 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 232 " --> pdb=" O LEU D 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 226 through 232' Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.691A pdb=" N SER E 37 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 41 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 80 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA E 85 " --> pdb=" O GLY E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA E 102 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 removed outlier: 3.630A pdb=" N GLN E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL E 188 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG E 198 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU E 229 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE E 230 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 231 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 226 through 232' Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA E 302 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 313 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 320 " --> pdb=" O GLY E 316 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG E 321 " --> pdb=" O ARG E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER F 37 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 41 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 80 Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA F 85 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 removed outlier: 3.632A pdb=" N GLN F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS F 165 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN F 205 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.706A pdb=" N LEU F 229 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE F 230 " --> pdb=" O ASP F 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 232 " --> pdb=" O LEU F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 226 through 232' Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 238 through 243 Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 268 " --> pdb=" O ASP F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA F 302 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 313 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN F 318 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 320 " --> pdb=" O GLY F 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG F 321 " --> pdb=" O ARG F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 41 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.936A pdb=" N ALA G 85 " --> pdb=" O GLY G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.654A pdb=" N THR G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'G' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL G 188 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 198 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN G 205 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU G 229 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE G 230 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G 231 " --> pdb=" O THR G 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 226 through 232' Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 238 through 243 Processing helix chain 'G' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU G 262 " --> pdb=" O THR G 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE G 265 " --> pdb=" O ASN G 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 268 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA G 302 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 313 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN G 318 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 321 " --> pdb=" O ARG G 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 31 through 49 removed outlier: 3.691A pdb=" N SER H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 41 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 80 Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA H 85 " --> pdb=" O GLY H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA H 102 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN H 153 " --> pdb=" O ALA H 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 155 " --> pdb=" O TYR H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 180 Processing helix chain 'H' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL H 188 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 198 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN H 205 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 209 " --> pdb=" O GLN H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU H 229 " --> pdb=" O GLN H 226 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE H 230 " --> pdb=" O ASP H 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 231 " --> pdb=" O THR H 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 232 " --> pdb=" O LEU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 226 through 232' Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 238 through 243 Processing helix chain 'H' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU H 262 " --> pdb=" O THR H 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU H 268 " --> pdb=" O ASP H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA H 302 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE H 313 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN H 318 " --> pdb=" O VAL H 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 320 " --> pdb=" O GLY H 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG H 321 " --> pdb=" O ARG H 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 3.623A pdb=" N TYR A 136 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 61 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR B 136 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 61 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR C 136 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 61 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR D 136 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 61 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR E 136 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 61 " --> pdb=" O VAL E 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR F 136 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 61 " --> pdb=" O VAL F 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR G 136 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 61 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.623A pdb=" N TYR H 136 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE H 61 " --> pdb=" O VAL H 281 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6528 1.34 - 1.46: 3625 1.46 - 1.58: 9311 1.58 - 1.70: 0 1.70 - 1.81: 112 Bond restraints: 19576 Sorted by residual: bond pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS H 31 " pdb=" CA LYS H 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS A 31 " pdb=" CA LYS A 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" N LYS C 31 " pdb=" CA LYS C 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.05e+01 ... (remaining 19571 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.58: 537 107.58 - 114.75: 11843 114.75 - 121.92: 10165 121.92 - 129.09: 3911 129.09 - 136.26: 56 Bond angle restraints: 26512 Sorted by residual: angle pdb=" N LEU E 27 " pdb=" CA LEU E 27 " pdb=" C LEU E 27 " ideal model delta sigma weight residual 111.07 102.19 8.88 1.07e+00 8.73e-01 6.89e+01 angle pdb=" N LEU C 27 " pdb=" CA LEU C 27 " pdb=" C LEU C 27 " ideal model delta sigma weight residual 111.07 102.20 8.87 1.07e+00 8.73e-01 6.88e+01 angle pdb=" N LEU G 27 " pdb=" CA LEU G 27 " pdb=" C LEU G 27 " ideal model delta sigma weight residual 111.07 102.20 8.87 1.07e+00 8.73e-01 6.87e+01 angle pdb=" N LEU A 27 " pdb=" CA LEU A 27 " pdb=" C LEU A 27 " ideal model delta sigma weight residual 111.07 102.21 8.86 1.07e+00 8.73e-01 6.85e+01 angle pdb=" N LEU B 27 " pdb=" CA LEU B 27 " pdb=" C LEU B 27 " ideal model delta sigma weight residual 111.07 102.21 8.86 1.07e+00 8.73e-01 6.85e+01 ... (remaining 26507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 10799 16.80 - 33.61: 1097 33.61 - 50.41: 200 50.41 - 67.21: 24 67.21 - 84.01: 40 Dihedral angle restraints: 12160 sinusoidal: 4944 harmonic: 7216 Sorted by residual: dihedral pdb=" CA TYR D 280 " pdb=" C TYR D 280 " pdb=" N VAL D 281 " pdb=" CA VAL D 281 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR H 280 " pdb=" C TYR H 280 " pdb=" N VAL H 281 " pdb=" CA VAL H 281 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR F 280 " pdb=" C TYR F 280 " pdb=" N VAL F 281 " pdb=" CA VAL F 281 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 12157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2327 0.052 - 0.104: 690 0.104 - 0.156: 111 0.156 - 0.207: 0 0.207 - 0.259: 16 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CA GLN C 26 " pdb=" N GLN C 26 " pdb=" C GLN C 26 " pdb=" CB GLN C 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLN A 26 " pdb=" N GLN A 26 " pdb=" C GLN A 26 " pdb=" CB GLN A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLN G 26 " pdb=" N GLN G 26 " pdb=" C GLN G 26 " pdb=" CB GLN G 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3141 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C LEU H 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU H 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL H 25 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C LEU A 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU A 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 25 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C LEU C 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU C 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 25 " 0.016 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7024 2.91 - 3.40: 18140 3.40 - 3.90: 28989 3.90 - 4.40: 34530 4.40 - 4.90: 56348 Nonbonded interactions: 145031 Sorted by model distance: nonbonded pdb=" O LEU F 23 " pdb=" OE1 GLN F 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU G 23 " pdb=" OE1 GLN G 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU C 23 " pdb=" OE1 GLN C 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU E 23 " pdb=" OE1 GLN E 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU A 23 " pdb=" OE1 GLN A 26 " model vdw 2.407 3.040 ... (remaining 145026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.650 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 48.470 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19576 Z= 0.281 Angle : 0.890 9.658 26512 Z= 0.513 Chirality : 0.050 0.259 3144 Planarity : 0.005 0.038 3432 Dihedral : 14.499 84.014 7488 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.38 % Allowed : 5.04 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.39 (0.11), residues: 2448 helix: -5.01 (0.04), residues: 1496 sheet: -3.47 (0.31), residues: 200 loop : -1.98 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 28 HIS 0.001 0.000 HIS C 243 PHE 0.007 0.002 PHE A 103 TYR 0.010 0.001 TYR D 81 ARG 0.002 0.000 ARG H 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 339 time to evaluate : 2.286 Fit side-chains REVERT: A 32 MET cc_start: 0.6567 (ttp) cc_final: 0.6091 (tmm) REVERT: A 139 GLN cc_start: 0.8255 (mt0) cc_final: 0.8050 (mt0) REVERT: A 153 GLN cc_start: 0.7820 (tt0) cc_final: 0.7584 (tp-100) REVERT: A 176 LYS cc_start: 0.8065 (tptt) cc_final: 0.7809 (ttpt) REVERT: B 32 MET cc_start: 0.6349 (ttp) cc_final: 0.5782 (tmm) REVERT: B 77 MET cc_start: 0.8351 (mmm) cc_final: 0.8112 (mmp) REVERT: B 90 ASP cc_start: 0.8269 (t0) cc_final: 0.8030 (m-30) REVERT: B 146 MET cc_start: 0.7694 (ttm) cc_final: 0.7466 (ttt) REVERT: B 147 LYS cc_start: 0.8238 (tppt) cc_final: 0.8035 (tptm) REVERT: B 176 LYS cc_start: 0.8021 (tptt) cc_final: 0.7681 (ttpp) REVERT: B 202 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 301 LEU cc_start: 0.8471 (mm) cc_final: 0.7997 (mm) REVERT: C 32 MET cc_start: 0.6603 (ttp) cc_final: 0.6166 (tmm) REVERT: C 139 GLN cc_start: 0.8272 (mt0) cc_final: 0.8061 (mt0) REVERT: C 146 MET cc_start: 0.7707 (ttm) cc_final: 0.7488 (ttt) REVERT: C 153 GLN cc_start: 0.7822 (tt0) cc_final: 0.7558 (tp-100) REVERT: C 176 LYS cc_start: 0.8093 (tptt) cc_final: 0.7792 (ttpt) REVERT: C 240 MET cc_start: 0.8721 (mtt) cc_final: 0.8510 (mtt) REVERT: D 32 MET cc_start: 0.6362 (ttp) cc_final: 0.5794 (tmm) REVERT: D 77 MET cc_start: 0.8359 (mmm) cc_final: 0.8121 (mmp) REVERT: D 90 ASP cc_start: 0.8270 (t0) cc_final: 0.8031 (m-30) REVERT: D 146 MET cc_start: 0.7696 (ttm) cc_final: 0.7476 (ttt) REVERT: D 147 LYS cc_start: 0.8239 (tppt) cc_final: 0.8026 (tptm) REVERT: D 176 LYS cc_start: 0.7981 (tptt) cc_final: 0.7633 (ttpp) REVERT: D 202 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 301 LEU cc_start: 0.8480 (mm) cc_final: 0.8031 (mm) REVERT: E 32 MET cc_start: 0.6583 (ttp) cc_final: 0.6134 (tmm) REVERT: E 139 GLN cc_start: 0.8272 (mt0) cc_final: 0.8064 (mt0) REVERT: E 146 MET cc_start: 0.7727 (ttm) cc_final: 0.7512 (ttt) REVERT: E 153 GLN cc_start: 0.7823 (tt0) cc_final: 0.7554 (tp-100) REVERT: E 176 LYS cc_start: 0.8057 (tptt) cc_final: 0.7759 (ttpt) REVERT: F 32 MET cc_start: 0.6356 (ttp) cc_final: 0.5786 (tmm) REVERT: F 77 MET cc_start: 0.8391 (mmm) cc_final: 0.8156 (mmp) REVERT: F 90 ASP cc_start: 0.8271 (t0) cc_final: 0.8029 (m-30) REVERT: F 146 MET cc_start: 0.7702 (ttm) cc_final: 0.7482 (ttt) REVERT: F 147 LYS cc_start: 0.8242 (tppt) cc_final: 0.8006 (tptm) REVERT: F 176 LYS cc_start: 0.7979 (tptt) cc_final: 0.7626 (ttpp) REVERT: F 202 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7156 (mm-30) REVERT: F 301 LEU cc_start: 0.8475 (mm) cc_final: 0.7996 (mm) REVERT: G 32 MET cc_start: 0.6569 (ttp) cc_final: 0.6091 (tmm) REVERT: G 139 GLN cc_start: 0.8263 (mt0) cc_final: 0.8057 (mt0) REVERT: G 153 GLN cc_start: 0.7829 (tt0) cc_final: 0.7574 (tp-100) REVERT: G 176 LYS cc_start: 0.8122 (tptt) cc_final: 0.7810 (ttpt) REVERT: H 32 MET cc_start: 0.6346 (ttp) cc_final: 0.5775 (tmm) REVERT: H 77 MET cc_start: 0.8381 (mmm) cc_final: 0.8148 (mmp) REVERT: H 90 ASP cc_start: 0.8270 (t0) cc_final: 0.8031 (m-30) REVERT: H 146 MET cc_start: 0.7673 (ttm) cc_final: 0.7437 (ttt) REVERT: H 147 LYS cc_start: 0.8255 (tppt) cc_final: 0.8020 (tptm) REVERT: H 176 LYS cc_start: 0.8022 (tptt) cc_final: 0.7679 (ttpp) REVERT: H 202 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7165 (mm-30) REVERT: H 301 LEU cc_start: 0.8462 (mm) cc_final: 0.7979 (mm) outliers start: 8 outliers final: 8 residues processed: 347 average time/residue: 1.2171 time to fit residues: 475.7412 Evaluate side-chains 200 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain H residue 28 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 0.0980 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 ASN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 ASN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19576 Z= 0.201 Angle : 0.533 6.827 26512 Z= 0.279 Chirality : 0.037 0.117 3144 Planarity : 0.003 0.019 3432 Dihedral : 6.030 54.038 2672 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.28 % Allowed : 15.11 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.13), residues: 2448 helix: -3.34 (0.09), residues: 1552 sheet: -2.30 (0.36), residues: 208 loop : -1.50 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 56 HIS 0.001 0.000 HIS B 243 PHE 0.007 0.001 PHE A 103 TYR 0.011 0.001 TYR B 73 ARG 0.002 0.000 ARG H 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 175 time to evaluate : 2.436 Fit side-chains REVERT: A 118 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7514 (ttmm) REVERT: A 139 GLN cc_start: 0.8305 (mt0) cc_final: 0.8074 (mt0) REVERT: A 202 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: B 301 LEU cc_start: 0.8390 (mm) cc_final: 0.8051 (mm) REVERT: C 118 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7501 (ttmm) REVERT: C 139 GLN cc_start: 0.8305 (mt0) cc_final: 0.8080 (mt0) REVERT: C 202 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: C 240 MET cc_start: 0.9013 (mtt) cc_final: 0.8787 (mtt) REVERT: D 301 LEU cc_start: 0.8462 (mm) cc_final: 0.8127 (mm) REVERT: E 118 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7504 (ttmm) REVERT: E 139 GLN cc_start: 0.8299 (mt0) cc_final: 0.8077 (mt0) REVERT: E 202 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: F 301 LEU cc_start: 0.8474 (mm) cc_final: 0.8158 (mm) REVERT: G 118 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7522 (ttmm) REVERT: G 139 GLN cc_start: 0.8310 (mt0) cc_final: 0.8087 (mt0) REVERT: G 202 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: H 147 LYS cc_start: 0.7858 (tppt) cc_final: 0.7577 (tptp) REVERT: H 301 LEU cc_start: 0.8424 (mm) cc_final: 0.8075 (mm) outliers start: 69 outliers final: 29 residues processed: 234 average time/residue: 1.1325 time to fit residues: 303.5437 Evaluate side-chains 173 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 87 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 218 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19576 Z= 0.260 Angle : 0.528 7.834 26512 Z= 0.268 Chirality : 0.037 0.113 3144 Planarity : 0.002 0.021 3432 Dihedral : 5.738 54.342 2672 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.61 % Allowed : 18.92 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.16), residues: 2448 helix: -2.13 (0.12), residues: 1584 sheet: -1.89 (0.39), residues: 200 loop : -1.02 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.002 0.000 HIS D 243 PHE 0.007 0.001 PHE C 103 TYR 0.011 0.001 TYR F 256 ARG 0.002 0.000 ARG E 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 159 time to evaluate : 2.238 Fit side-chains REVERT: A 28 TRP cc_start: 0.9276 (OUTLIER) cc_final: 0.8349 (t60) REVERT: A 118 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7542 (ttmm) REVERT: A 139 GLN cc_start: 0.8313 (mt0) cc_final: 0.7903 (mt0) REVERT: A 202 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: B 28 TRP cc_start: 0.9300 (OUTLIER) cc_final: 0.8455 (t60) REVERT: B 222 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 301 LEU cc_start: 0.8166 (mm) cc_final: 0.7776 (mm) REVERT: C 28 TRP cc_start: 0.9292 (OUTLIER) cc_final: 0.8366 (t60) REVERT: C 118 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7560 (ttmm) REVERT: C 139 GLN cc_start: 0.8323 (mt0) cc_final: 0.7929 (mt0) REVERT: C 202 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: D 28 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8457 (t60) REVERT: D 222 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: D 301 LEU cc_start: 0.8180 (mm) cc_final: 0.7791 (mm) REVERT: E 28 TRP cc_start: 0.9270 (OUTLIER) cc_final: 0.8406 (t60) REVERT: E 118 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7555 (ttmm) REVERT: E 139 GLN cc_start: 0.8325 (mt0) cc_final: 0.7931 (mt0) REVERT: E 202 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: F 28 TRP cc_start: 0.9295 (OUTLIER) cc_final: 0.8463 (t60) REVERT: F 222 GLU cc_start: 0.7391 (mp0) cc_final: 0.7189 (mp0) REVERT: F 301 LEU cc_start: 0.8189 (mm) cc_final: 0.7796 (mm) REVERT: G 28 TRP cc_start: 0.9275 (OUTLIER) cc_final: 0.8351 (t60) REVERT: G 118 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7552 (ttmm) REVERT: G 139 GLN cc_start: 0.8313 (mt0) cc_final: 0.7908 (mt0) REVERT: G 202 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: H 28 TRP cc_start: 0.9290 (OUTLIER) cc_final: 0.8448 (t60) REVERT: H 146 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7240 (ttt) REVERT: H 301 LEU cc_start: 0.8152 (mm) cc_final: 0.7752 (mm) outliers start: 76 outliers final: 26 residues processed: 208 average time/residue: 1.2936 time to fit residues: 302.7039 Evaluate side-chains 184 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 139 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19576 Z= 0.209 Angle : 0.503 7.480 26512 Z= 0.251 Chirality : 0.037 0.111 3144 Planarity : 0.002 0.017 3432 Dihedral : 5.489 53.797 2672 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.80 % Allowed : 19.58 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2448 helix: -1.45 (0.13), residues: 1600 sheet: -1.27 (0.39), residues: 208 loop : -0.61 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 56 HIS 0.001 0.000 HIS B 243 PHE 0.006 0.001 PHE E 103 TYR 0.008 0.001 TYR F 73 ARG 0.001 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 157 time to evaluate : 2.312 Fit side-chains REVERT: A 28 TRP cc_start: 0.9233 (OUTLIER) cc_final: 0.8552 (t60) REVERT: A 118 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7541 (ttmm) REVERT: A 139 GLN cc_start: 0.8291 (mt0) cc_final: 0.7846 (mt0) REVERT: A 202 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: A 274 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: B 28 TRP cc_start: 0.9268 (OUTLIER) cc_final: 0.8598 (t60) REVERT: B 32 MET cc_start: 0.7100 (tpp) cc_final: 0.6832 (tpp) REVERT: B 77 MET cc_start: 0.8107 (mmm) cc_final: 0.7820 (mmp) REVERT: B 222 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: B 301 LEU cc_start: 0.8056 (mm) cc_final: 0.7626 (mm) REVERT: C 28 TRP cc_start: 0.9234 (OUTLIER) cc_final: 0.8549 (t60) REVERT: C 118 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7553 (ttmm) REVERT: C 139 GLN cc_start: 0.8294 (mt0) cc_final: 0.7856 (mt0) REVERT: C 202 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 222 GLU cc_start: 0.7902 (tp30) cc_final: 0.7482 (mp0) REVERT: C 274 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: C 301 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7900 (mm) REVERT: D 28 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8610 (t60) REVERT: D 32 MET cc_start: 0.7111 (tpp) cc_final: 0.6838 (tpp) REVERT: D 77 MET cc_start: 0.8130 (mmm) cc_final: 0.7839 (mmp) REVERT: D 222 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: D 301 LEU cc_start: 0.8075 (mm) cc_final: 0.7664 (mm) REVERT: E 28 TRP cc_start: 0.9229 (OUTLIER) cc_final: 0.8606 (t60) REVERT: E 118 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7556 (ttmm) REVERT: E 202 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: E 222 GLU cc_start: 0.7955 (tp30) cc_final: 0.7471 (mp0) REVERT: F 28 TRP cc_start: 0.9259 (OUTLIER) cc_final: 0.8602 (t60) REVERT: F 32 MET cc_start: 0.7102 (tpp) cc_final: 0.6819 (tpp) REVERT: F 77 MET cc_start: 0.8130 (mmm) cc_final: 0.7842 (mmp) REVERT: F 301 LEU cc_start: 0.8038 (mm) cc_final: 0.7613 (mm) REVERT: G 28 TRP cc_start: 0.9228 (OUTLIER) cc_final: 0.8593 (t60) REVERT: G 118 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7546 (ttmm) REVERT: G 139 GLN cc_start: 0.8292 (mt0) cc_final: 0.7850 (mt0) REVERT: G 202 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: H 28 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8601 (t60) REVERT: H 32 MET cc_start: 0.7107 (tpp) cc_final: 0.6831 (tpp) REVERT: H 77 MET cc_start: 0.8111 (mmm) cc_final: 0.7825 (mmp) REVERT: H 146 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7195 (ttt) REVERT: H 301 LEU cc_start: 0.8043 (mm) cc_final: 0.7623 (mm) outliers start: 80 outliers final: 28 residues processed: 217 average time/residue: 1.1576 time to fit residues: 286.5254 Evaluate side-chains 196 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS F 260 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 19576 Z= 0.294 Angle : 0.525 8.403 26512 Z= 0.264 Chirality : 0.038 0.114 3144 Planarity : 0.002 0.024 3432 Dihedral : 5.500 53.218 2672 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.94 % Allowed : 20.39 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2448 helix: -1.10 (0.13), residues: 1600 sheet: -1.18 (0.40), residues: 200 loop : -0.47 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 56 HIS 0.002 0.001 HIS F 243 PHE 0.006 0.001 PHE F 251 TYR 0.010 0.001 TYR E 256 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 151 time to evaluate : 2.281 Fit side-chains REVERT: A 28 TRP cc_start: 0.9217 (OUTLIER) cc_final: 0.8642 (t60) REVERT: A 118 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7534 (ttmm) REVERT: A 202 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: A 222 GLU cc_start: 0.7861 (tp30) cc_final: 0.7296 (mp0) REVERT: B 28 TRP cc_start: 0.9260 (OUTLIER) cc_final: 0.8694 (t60) REVERT: B 301 LEU cc_start: 0.7980 (mm) cc_final: 0.7505 (mm) REVERT: C 28 TRP cc_start: 0.9245 (OUTLIER) cc_final: 0.8680 (t60) REVERT: C 118 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7544 (ttmm) REVERT: C 202 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: C 222 GLU cc_start: 0.7964 (tp30) cc_final: 0.7316 (mt-10) REVERT: C 274 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: C 301 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7918 (mm) REVERT: D 28 TRP cc_start: 0.9252 (OUTLIER) cc_final: 0.8710 (t60) REVERT: D 222 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: D 301 LEU cc_start: 0.7993 (mm) cc_final: 0.7516 (mm) REVERT: E 28 TRP cc_start: 0.9226 (OUTLIER) cc_final: 0.8690 (t60) REVERT: E 118 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7545 (ttmm) REVERT: E 202 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: E 222 GLU cc_start: 0.8023 (tp30) cc_final: 0.7500 (mp0) REVERT: F 28 TRP cc_start: 0.9248 (OUTLIER) cc_final: 0.8718 (t60) REVERT: F 260 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7826 (tp40) REVERT: F 301 LEU cc_start: 0.7982 (mm) cc_final: 0.7502 (mm) REVERT: G 28 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.8638 (t60) REVERT: G 118 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7536 (ttmm) REVERT: G 202 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: G 222 GLU cc_start: 0.7876 (tp30) cc_final: 0.7449 (mp0) REVERT: H 28 TRP cc_start: 0.9247 (OUTLIER) cc_final: 0.8681 (t60) REVERT: H 222 GLU cc_start: 0.7356 (mp0) cc_final: 0.7101 (mp0) REVERT: H 301 LEU cc_start: 0.7967 (mm) cc_final: 0.7483 (mm) outliers start: 104 outliers final: 34 residues processed: 229 average time/residue: 1.0553 time to fit residues: 278.8117 Evaluate side-chains 192 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 0.4980 chunk 107 optimal weight: 0.0670 chunk 19 optimal weight: 0.4980 chunk 76 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 19576 Z= 0.148 Angle : 0.475 9.313 26512 Z= 0.237 Chirality : 0.036 0.123 3144 Planarity : 0.002 0.014 3432 Dihedral : 5.222 52.728 2672 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.04 % Allowed : 22.62 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2448 helix: -0.61 (0.14), residues: 1592 sheet: -0.90 (0.39), residues: 208 loop : -0.28 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 28 HIS 0.001 0.000 HIS C 243 PHE 0.005 0.001 PHE C 103 TYR 0.006 0.001 TYR H 73 ARG 0.001 0.000 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 157 time to evaluate : 2.247 Fit side-chains REVERT: A 28 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.8767 (t60) REVERT: A 118 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7535 (ttmm) REVERT: A 130 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7880 (mt) REVERT: A 139 GLN cc_start: 0.8273 (mt0) cc_final: 0.7832 (mt0) REVERT: A 202 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: A 244 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: B 28 TRP cc_start: 0.9268 (OUTLIER) cc_final: 0.8894 (t60) REVERT: B 32 MET cc_start: 0.7056 (tpp) cc_final: 0.6853 (tpp) REVERT: B 77 MET cc_start: 0.8116 (mmm) cc_final: 0.7784 (mmp) REVERT: C 28 TRP cc_start: 0.9205 (OUTLIER) cc_final: 0.8786 (t60) REVERT: C 118 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7542 (ttmm) REVERT: C 130 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7917 (mt) REVERT: C 139 GLN cc_start: 0.8275 (mt0) cc_final: 0.7839 (mt0) REVERT: C 202 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: C 218 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6493 (mt0) REVERT: C 222 GLU cc_start: 0.7819 (tp30) cc_final: 0.7502 (mp0) REVERT: C 244 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: D 28 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.8912 (t60) REVERT: D 77 MET cc_start: 0.8131 (mmm) cc_final: 0.7814 (mmp) REVERT: D 222 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: D 260 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7841 (tp40) REVERT: E 28 TRP cc_start: 0.9192 (OUTLIER) cc_final: 0.8779 (t60) REVERT: E 118 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7541 (ttmm) REVERT: E 130 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7911 (mt) REVERT: E 139 GLN cc_start: 0.8279 (mt0) cc_final: 0.7842 (mt0) REVERT: E 202 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: E 222 GLU cc_start: 0.7883 (tp30) cc_final: 0.7424 (mp0) REVERT: F 28 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.8899 (t60) REVERT: F 32 MET cc_start: 0.7074 (tpp) cc_final: 0.6858 (tpp) REVERT: F 77 MET cc_start: 0.8129 (mmm) cc_final: 0.7813 (mmp) REVERT: F 260 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7789 (tp40) REVERT: G 28 TRP cc_start: 0.9194 (OUTLIER) cc_final: 0.8772 (t60) REVERT: G 32 MET cc_start: 0.6835 (tpp) cc_final: 0.6609 (tpp) REVERT: G 118 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7539 (ttmm) REVERT: G 130 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7852 (mt) REVERT: G 139 GLN cc_start: 0.8272 (mt0) cc_final: 0.7834 (mt0) REVERT: G 202 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: G 222 GLU cc_start: 0.7910 (tp30) cc_final: 0.7390 (mp0) REVERT: H 28 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.8899 (t60) REVERT: H 32 MET cc_start: 0.7063 (tpp) cc_final: 0.6853 (tpp) REVERT: H 77 MET cc_start: 0.8125 (mmm) cc_final: 0.7811 (mmp) REVERT: H 222 GLU cc_start: 0.7509 (mp0) cc_final: 0.7290 (mp0) outliers start: 64 outliers final: 24 residues processed: 202 average time/residue: 1.2030 time to fit residues: 275.8559 Evaluate side-chains 189 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 139 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 225 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 144 optimal weight: 0.0870 chunk 141 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19576 Z= 0.175 Angle : 0.482 10.111 26512 Z= 0.240 Chirality : 0.036 0.111 3144 Planarity : 0.002 0.015 3432 Dihedral : 5.149 52.305 2672 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.85 % Allowed : 22.81 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2448 helix: -0.32 (0.14), residues: 1592 sheet: -0.58 (0.39), residues: 200 loop : -0.33 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 56 HIS 0.000 0.000 HIS E 243 PHE 0.007 0.001 PHE C 103 TYR 0.008 0.001 TYR D 256 ARG 0.001 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 153 time to evaluate : 2.342 Fit side-chains REVERT: A 28 TRP cc_start: 0.9208 (OUTLIER) cc_final: 0.8861 (t60) REVERT: A 118 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: A 139 GLN cc_start: 0.8263 (mt0) cc_final: 0.7813 (mt0) REVERT: A 202 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: A 244 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: A 260 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7953 (tp40) REVERT: B 28 TRP cc_start: 0.9280 (OUTLIER) cc_final: 0.8951 (t60) REVERT: B 77 MET cc_start: 0.8141 (mmm) cc_final: 0.7825 (mmp) REVERT: B 222 GLU cc_start: 0.7415 (mp0) cc_final: 0.6876 (mp0) REVERT: B 260 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7802 (tp40) REVERT: C 28 TRP cc_start: 0.9213 (OUTLIER) cc_final: 0.8863 (t60) REVERT: C 118 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7563 (ttmm) REVERT: C 130 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7864 (mt) REVERT: C 139 GLN cc_start: 0.8268 (mt0) cc_final: 0.7822 (mt0) REVERT: C 202 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: C 244 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: C 260 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7944 (tp40) REVERT: C 301 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7709 (mm) REVERT: D 28 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8949 (t60) REVERT: D 77 MET cc_start: 0.8155 (mmm) cc_final: 0.7840 (mmp) REVERT: E 28 TRP cc_start: 0.9198 (OUTLIER) cc_final: 0.8835 (t60) REVERT: E 118 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7557 (ttmm) REVERT: E 130 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7859 (mt) REVERT: E 139 GLN cc_start: 0.8283 (mt0) cc_final: 0.7844 (mt0) REVERT: E 260 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: E 301 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7611 (mm) REVERT: F 28 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.8945 (t60) REVERT: F 32 MET cc_start: 0.7061 (tpp) cc_final: 0.6860 (tpp) REVERT: F 77 MET cc_start: 0.8156 (mmm) cc_final: 0.7843 (mmp) REVERT: F 222 GLU cc_start: 0.7589 (mp0) cc_final: 0.7122 (mp0) REVERT: F 260 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7847 (tp40) REVERT: G 28 TRP cc_start: 0.9207 (OUTLIER) cc_final: 0.8868 (t60) REVERT: G 32 MET cc_start: 0.6893 (tpp) cc_final: 0.6673 (tpp) REVERT: G 118 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7560 (ttmm) REVERT: G 139 GLN cc_start: 0.8265 (mt0) cc_final: 0.7818 (mt0) REVERT: G 202 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: G 222 GLU cc_start: 0.7781 (tp30) cc_final: 0.7528 (mp0) REVERT: G 260 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7947 (tp40) REVERT: H 28 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.8939 (t60) REVERT: H 32 MET cc_start: 0.7022 (tpp) cc_final: 0.6800 (tpp) REVERT: H 77 MET cc_start: 0.8153 (mmm) cc_final: 0.7841 (mmp) REVERT: H 222 GLU cc_start: 0.7481 (mp0) cc_final: 0.7275 (mp0) REVERT: H 260 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7804 (tp40) outliers start: 81 outliers final: 24 residues processed: 212 average time/residue: 1.2496 time to fit residues: 300.1118 Evaluate side-chains 195 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 143 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 146 MET Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 260 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19576 Z= 0.177 Angle : 0.493 11.037 26512 Z= 0.243 Chirality : 0.036 0.111 3144 Planarity : 0.002 0.015 3432 Dihedral : 5.090 51.992 2672 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.99 % Allowed : 24.29 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 2448 helix: -0.05 (0.14), residues: 1592 sheet: -0.46 (0.40), residues: 200 loop : -0.29 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 56 HIS 0.001 0.000 HIS A 243 PHE 0.006 0.001 PHE G 103 TYR 0.008 0.001 TYR F 256 ARG 0.002 0.000 ARG F 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 155 time to evaluate : 2.365 Fit side-chains REVERT: A 28 TRP cc_start: 0.9194 (OUTLIER) cc_final: 0.8849 (t60) REVERT: A 118 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7580 (ttmm) REVERT: A 139 GLN cc_start: 0.8272 (mt0) cc_final: 0.7835 (mt0) REVERT: A 202 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: A 218 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6696 (mt0) REVERT: A 244 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: A 260 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7975 (tp40) REVERT: B 28 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8950 (t60) REVERT: B 77 MET cc_start: 0.8072 (mmm) cc_final: 0.7738 (mmp) REVERT: B 130 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8068 (pp) REVERT: B 222 GLU cc_start: 0.7538 (mp0) cc_final: 0.7105 (mp0) REVERT: C 28 TRP cc_start: 0.9200 (OUTLIER) cc_final: 0.8850 (t60) REVERT: C 118 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7582 (ttmm) REVERT: C 139 GLN cc_start: 0.8268 (mt0) cc_final: 0.7839 (mt0) REVERT: C 244 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: C 260 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7943 (tp40) REVERT: D 28 TRP cc_start: 0.9265 (OUTLIER) cc_final: 0.8949 (t60) REVERT: D 77 MET cc_start: 0.8088 (mmm) cc_final: 0.7754 (mmp) REVERT: D 130 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8081 (pp) REVERT: E 28 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.8861 (t60) REVERT: E 118 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7561 (ttmm) REVERT: E 139 GLN cc_start: 0.8275 (mt0) cc_final: 0.7842 (mt0) REVERT: E 222 GLU cc_start: 0.7902 (tp30) cc_final: 0.7667 (mp0) REVERT: E 260 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: F 28 TRP cc_start: 0.9257 (OUTLIER) cc_final: 0.8943 (t60) REVERT: F 77 MET cc_start: 0.8090 (mmm) cc_final: 0.7754 (mmp) REVERT: F 130 LEU cc_start: 0.8297 (pp) cc_final: 0.8002 (mp) REVERT: F 222 GLU cc_start: 0.7724 (mp0) cc_final: 0.7319 (mp0) REVERT: G 28 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.8855 (t60) REVERT: G 32 MET cc_start: 0.6878 (tpp) cc_final: 0.6645 (tpp) REVERT: G 118 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7576 (ttmm) REVERT: G 139 GLN cc_start: 0.8264 (mt0) cc_final: 0.7836 (mt0) REVERT: G 222 GLU cc_start: 0.7781 (tp30) cc_final: 0.7529 (mp0) REVERT: G 260 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: H 28 TRP cc_start: 0.9259 (OUTLIER) cc_final: 0.8945 (t60) REVERT: H 32 MET cc_start: 0.7048 (tpp) cc_final: 0.6845 (tpp) REVERT: H 77 MET cc_start: 0.8085 (mmm) cc_final: 0.7751 (mmp) REVERT: H 130 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7990 (mp) REVERT: H 222 GLU cc_start: 0.7490 (mp0) cc_final: 0.7276 (mp0) outliers start: 63 outliers final: 26 residues processed: 199 average time/residue: 1.1677 time to fit residues: 264.8417 Evaluate side-chains 194 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 145 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 8.9990 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19576 Z= 0.181 Angle : 0.505 11.642 26512 Z= 0.247 Chirality : 0.036 0.112 3144 Planarity : 0.002 0.015 3432 Dihedral : 5.043 51.609 2672 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.85 % Allowed : 24.71 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2448 helix: 0.16 (0.14), residues: 1592 sheet: -0.34 (0.40), residues: 200 loop : -0.26 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 56 HIS 0.001 0.000 HIS C 276 PHE 0.006 0.001 PHE E 103 TYR 0.007 0.001 TYR F 256 ARG 0.003 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 148 time to evaluate : 2.320 Fit side-chains REVERT: A 28 TRP cc_start: 0.9219 (OUTLIER) cc_final: 0.8903 (t60) REVERT: A 118 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7563 (ttmm) REVERT: A 139 GLN cc_start: 0.8265 (mt0) cc_final: 0.7814 (mt0) REVERT: A 202 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: A 244 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: B 28 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8979 (t60) REVERT: B 77 MET cc_start: 0.8049 (mmm) cc_final: 0.7762 (mmp) REVERT: B 130 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8077 (pp) REVERT: B 222 GLU cc_start: 0.7527 (mp0) cc_final: 0.7163 (mp0) REVERT: C 28 TRP cc_start: 0.9223 (OUTLIER) cc_final: 0.8904 (t60) REVERT: C 118 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7582 (ttmm) REVERT: C 139 GLN cc_start: 0.8260 (mt0) cc_final: 0.7819 (mt0) REVERT: C 222 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7423 (mp0) REVERT: C 274 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: D 28 TRP cc_start: 0.9270 (OUTLIER) cc_final: 0.8979 (t60) REVERT: D 77 MET cc_start: 0.8084 (mmm) cc_final: 0.7797 (mmp) REVERT: D 130 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8092 (pp) REVERT: E 28 TRP cc_start: 0.9216 (OUTLIER) cc_final: 0.8916 (t60) REVERT: E 118 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7545 (ttmm) REVERT: E 139 GLN cc_start: 0.8271 (mt0) cc_final: 0.7839 (mt0) REVERT: E 222 GLU cc_start: 0.7881 (tp30) cc_final: 0.7644 (mp0) REVERT: E 301 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7521 (mm) REVERT: F 28 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8973 (t60) REVERT: F 77 MET cc_start: 0.8084 (mmm) cc_final: 0.7798 (mmp) REVERT: F 130 LEU cc_start: 0.8297 (pp) cc_final: 0.8009 (mp) REVERT: F 222 GLU cc_start: 0.7652 (mp0) cc_final: 0.7320 (mp0) REVERT: G 28 TRP cc_start: 0.9213 (OUTLIER) cc_final: 0.8908 (t60) REVERT: G 32 MET cc_start: 0.6920 (tpp) cc_final: 0.6674 (tpp) REVERT: G 118 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7575 (ttmm) REVERT: G 139 GLN cc_start: 0.8261 (mt0) cc_final: 0.7835 (mt0) REVERT: G 222 GLU cc_start: 0.7775 (tp30) cc_final: 0.7555 (mp0) REVERT: H 28 TRP cc_start: 0.9262 (OUTLIER) cc_final: 0.8975 (t60) REVERT: H 32 MET cc_start: 0.7068 (tpp) cc_final: 0.6866 (tpp) REVERT: H 77 MET cc_start: 0.8085 (mmm) cc_final: 0.7753 (mmp) REVERT: H 130 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7992 (mp) REVERT: H 222 GLU cc_start: 0.7488 (mp0) cc_final: 0.7210 (mp0) REVERT: H 260 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7782 (tp40) outliers start: 60 outliers final: 28 residues processed: 189 average time/residue: 1.1978 time to fit residues: 257.5268 Evaluate side-chains 194 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 146 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 260 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.5980 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 GLN H 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19576 Z= 0.179 Angle : 0.508 12.225 26512 Z= 0.248 Chirality : 0.036 0.111 3144 Planarity : 0.002 0.016 3432 Dihedral : 5.004 51.234 2672 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.61 % Allowed : 24.81 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2448 helix: 0.36 (0.14), residues: 1592 sheet: -0.29 (0.40), residues: 200 loop : -0.25 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 56 HIS 0.001 0.000 HIS C 243 PHE 0.006 0.001 PHE E 103 TYR 0.008 0.001 TYR F 256 ARG 0.001 0.000 ARG C 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 2.421 Fit side-chains REVERT: A 28 TRP cc_start: 0.9218 (OUTLIER) cc_final: 0.8924 (t60) REVERT: A 139 GLN cc_start: 0.8261 (mt0) cc_final: 0.7809 (mt0) REVERT: A 222 GLU cc_start: 0.7533 (mp0) cc_final: 0.7164 (mp0) REVERT: A 244 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: A 260 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7932 (tp40) REVERT: B 28 TRP cc_start: 0.9248 (OUTLIER) cc_final: 0.8976 (t60) REVERT: B 77 MET cc_start: 0.8035 (mmm) cc_final: 0.7741 (mmp) REVERT: B 130 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 222 GLU cc_start: 0.7583 (mp0) cc_final: 0.7181 (mp0) REVERT: C 28 TRP cc_start: 0.9227 (OUTLIER) cc_final: 0.8940 (t60) REVERT: C 139 GLN cc_start: 0.8257 (mt0) cc_final: 0.7815 (mt0) REVERT: C 260 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: C 274 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: D 28 TRP cc_start: 0.9243 (OUTLIER) cc_final: 0.8977 (t60) REVERT: D 77 MET cc_start: 0.8085 (mmm) cc_final: 0.7803 (mmp) REVERT: D 130 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7999 (mp) REVERT: E 28 TRP cc_start: 0.9212 (OUTLIER) cc_final: 0.8902 (t60) REVERT: E 118 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7521 (ttmm) REVERT: E 139 GLN cc_start: 0.8265 (mt0) cc_final: 0.7819 (mt0) REVERT: E 222 GLU cc_start: 0.7880 (tp30) cc_final: 0.7661 (mp0) REVERT: E 260 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7895 (tp40) REVERT: F 28 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.8940 (t60) REVERT: F 77 MET cc_start: 0.8070 (mmm) cc_final: 0.7786 (mmp) REVERT: F 130 LEU cc_start: 0.8297 (pp) cc_final: 0.8012 (mp) REVERT: F 222 GLU cc_start: 0.7612 (mp0) cc_final: 0.7291 (mp0) REVERT: G 28 TRP cc_start: 0.9208 (OUTLIER) cc_final: 0.8893 (t60) REVERT: G 32 MET cc_start: 0.6949 (tpp) cc_final: 0.6700 (tpp) REVERT: G 118 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7547 (ttmm) REVERT: G 139 GLN cc_start: 0.8255 (mt0) cc_final: 0.7814 (mt0) REVERT: G 260 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7902 (tp40) REVERT: H 28 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.8942 (t60) REVERT: H 77 MET cc_start: 0.8087 (mmm) cc_final: 0.7808 (mmp) REVERT: H 130 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7991 (mp) REVERT: H 260 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7752 (tp40) outliers start: 55 outliers final: 26 residues processed: 194 average time/residue: 1.1873 time to fit residues: 262.0073 Evaluate side-chains 195 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 149 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 28 TRP Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 28 TRP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 28 TRP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 260 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 0.3980 chunk 58 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 195 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN C 205 GLN C 260 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097870 restraints weight = 25151.965| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.25 r_work: 0.3061 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19576 Z= 0.133 Angle : 0.495 12.221 26512 Z= 0.241 Chirality : 0.035 0.110 3144 Planarity : 0.002 0.014 3432 Dihedral : 4.895 50.882 2672 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.19 % Allowed : 25.33 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2448 helix: 0.75 (0.15), residues: 1568 sheet: -0.31 (0.39), residues: 200 loop : -0.27 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 28 HIS 0.000 0.000 HIS B 243 PHE 0.006 0.001 PHE E 103 TYR 0.006 0.001 TYR H 256 ARG 0.001 0.000 ARG A 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5744.65 seconds wall clock time: 102 minutes 30.09 seconds (6150.09 seconds total)